Analyze and visualize VDJ data with Seurat
Author: Biqing Li
May 6, 2020
Outline
- Seurat scRNA standard analysis
- Quality Control
- Normalization
- Highly variable gene
- PCA
- UMAP & TSNE
- cell type annotation
- Consolidate VDJ information
- Paired B and T cells
- B cell and BCR
- T cell and TCR
- B cell VDJ genotype
- gamma delta T cell VDJ genotype
Quality control
Highly variable genes
PCA
UMAP
|
|
0
|
1
|
2
|
3
|
4
|
5
|
6
|
7
|
8
|
9
|
|
cell.freq
|
0.24
|
0.24
|
0.17
|
0.11
|
0.1
|
0.07
|
0.03
|
0.01
|
0.01
|
0.01
|
|
cell.num
|
641.00
|
636.00
|
451.00
|
280.00
|
257.0
|
176.00
|
78.00
|
38.00
|
38.00
|
22.00
|
TSNE
Markers for each cluster
|
cluster0
|
cluster1
|
cluster2
|
cluster3
|
cluster4
|
cluster5
|
cluster6
|
cluster7
|
cluster8
|
cluster9
|
|
IL7R
|
GNLY
|
S100A9
|
CD8B
|
IGKC
|
CXCR3
|
C1QA
|
CCR7
|
MCM2
|
FCER1A
|
|
PIK3IP1
|
KLRF1
|
S100A12
|
CD8A
|
IGHM-membrane
|
GZMK
|
IL3RA
|
IL7R
|
TYMS
|
CLEC10A
|
|
LEF1
|
GZMB
|
CD14
|
KLRK1
|
CD79A
|
IL32
|
PTGDR2
|
PIK3IP1
|
TRAT1
|
FLT3
|
|
TCF7
|
PRF1
|
IER3
|
CCL5
|
IGHD-membrane
|
IL7R
|
TNFRSF8
|
LTB
|
PIK3IP1
|
CD1C
|
|
CCR7
|
IL2RB
|
FCN1
|
TARP-refseq
|
IGHM-secreted
|
CD3E
|
CXCL16
|
LEF1
|
TCF7
|
IL18
|
|
CD6
|
NKG7
|
CXCL8
|
GZMK
|
MS4A1
|
CD2.1
|
FCGR3A
|
CD6
|
LEF1
|
HLA-DRA
|
|
CD5
|
TBX21
|
CLEC4E
|
IL32
|
CD22
|
CD6
|
LYN
|
CD3D
|
GIMAP2
|
CD33
|
|
CD27
|
TRDC
|
CD163
|
GZMH
|
VPREB3
|
CD3D
|
BCL2A1
|
GIMAP5
|
TRIB2
|
HLA-DQB1
|
|
LTB
|
IL18RAP
|
CD36
|
GZMA
|
IGLC3
|
LTB
|
PIK3AP1
|
PASK
|
MYC
|
HLA-DMA
|
|
MYC
|
CD160
|
CCL3
|
KLRG1
|
TCL1A
|
CD3G
|
IFITM3
|
MYC
|
PCNA
|
HLA-DPA1
|
Violin plot for classical markers
Dotplot plot for classical markers
RidgePlot plot for classical markers
Feature plot for classical markers
Assigning cell type identity to clusters
Heatmap
3D UMAP gif
All paired B & T cells
B cell & BCR
T_CD4_memory & TCR
T_CD4_naive & TCR
T_CD8_memory & TCR
T_CD8_naive & TCR
T_gamma_delta & TCR
B cell VDJ genotype
Gamma delta T cell VDJ genotype
